Lithium-ion batteries offer advantages as an energy storage unit for flight vehicles: they have high energy density, adequate power density, and they offer good cycle life compared to other high energy density storage types. One large drawback, however, is the fire danger they pose. Due to their high power density, lithium ion cells can burn or explode vigorously if they reach their thermal runaway temperature by shorting, external heating, or some other defect. The presence of oxidizer and fuel inside the battery cell means combustion temperatures are hot and the reaction is difficult to stop once started.
In flight vehicles it is desirable to minimize weight, meaning that fire suppression is difficult because the weight of systems to contain or extinguish a battery fire can be prohibitive. Large quantities of thermal damping material such as water would be required to moderate the temperature of battery cells so they would not go into thermal runaway. A strong pressure vessel would also be needed to contain the heat and gas generated by a fire, but again this would be heavy and significantly detract from the high energy density that makes lithium ion batteries an attractive energy storage method.
In a flight vehicle that must have very low weight and whose structure is very sensitive to damage, if the batteries were contained inside the vehicle structure, the hot and corrosive combustion products would have to be fully contained until they could be ducted outside of the vehicle. Even a small containment vessel failure could cause structural failure and result in a vehicle crash.